SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_13_1.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.6.10
Cutadapt version: 4.9
Python version: could not detect
Number of cores used for trimming: 8
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Unable to auto-detect most prominent adapter from the first specified file (count smallRNA: 0, count Nextera: 0, count Illumina: 0)
Defaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior).
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Running FastQC on the data once trimming has completed
Output file will be GZIP compressed


This is cutadapt 4.9 with Python 3.12.8
Command line parameters: -j 8 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr3644_13_1.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 200.528 s (3.762 µs/read; 15.95 M reads/minute).

=== Summary ===

Total reads processed:              53,303,436
Reads with adapters:                11,774,395 (22.1%)
Reads written (passing filters):    53,303,436 (100.0%)

Total basepairs processed: 5,648,038,153 bp
Quality-trimmed:               1,056,778 bp (0.0%)
Total written (filtered):  5,634,111,947 bp (99.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11774395 times

Minimum overlap: 1
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 47.9%
  C: 11.3%
  G: 6.0%
  T: 34.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	11302779	13325859.0	0	11302779
2	11430	3331464.8	0	11430
3	298243	832866.2	0	298243
4	161214	208216.5	0	161214
5	620	52054.1	0	620
6	5	13013.5	0	5
7	4	3253.4	0	4
9	4	203.3	0	2 2
10	47	50.8	1	0 47
11	48	12.7	1	0 48
12	1	3.2	1	0 1

RUN STATISTICS FOR INPUT FILE: zr3644_13_1.fastq.gz
=============================================
53303436 sequences processed in total